components

Bindings for protocols::denovo_design::components namespace

class pyrosetta.rosetta.protocols.denovo_design.components.Alias

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.Alias, : pyrosetta.rosetta.protocols.denovo_design.components.Alias) pyrosetta.rosetta.protocols.denovo_design.components.Alias

C++: protocols::denovo_design::components::Alias::operator=(const class protocols::denovo_design::components::Alias &) –> class protocols::denovo_design::components::Alias &

class pyrosetta.rosetta.protocols.denovo_design.components.BondInfo

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.BondInfo, : pyrosetta.rosetta.protocols.denovo_design.components.BondInfo) pyrosetta.rosetta.protocols.denovo_design.components.BondInfo

C++: protocols::denovo_design::components::BondInfo::operator=(const class protocols::denovo_design::components::BondInfo &) –> class protocols::denovo_design::components::BondInfo &

property atom1
property atom2
property res1
property res2
property seg1
property seg2
class pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases

Bases: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t

append(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: pyrosetta.rosetta.std.vector_std_string) None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases, : pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases) pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases

C++: protocols::denovo_design::components::BuildPhases::operator=(const class protocols::denovo_design::components::BuildPhases &) –> class protocols::denovo_design::components::BuildPhases &

back(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) pyrosetta.rosetta.std.vector_std_string

access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) None

clears the contents

count(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: pyrosetta.rosetta.std.vector_std_string) int

counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: int) None

erases element at index

extend(othervec)
front(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) pyrosetta.rosetta.std.vector_std_string

access the first element

l(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) -> pyrosetta.rosetta.std.vector_std_string

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: int) -> pyrosetta.rosetta.std.vector_std_string

remove and return item at index

remove(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: pyrosetta.rosetta.std.vector_std_string) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: int) None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t, arg0: int) None

changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_std_vector_std_string_t) int

upper index

class pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

“mutates” a set of mixed architects

add_perturber(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, perturber: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) None

Add a sub-perturber. Based on the mode, one or all of the perturbers will be called every time a perturbation is requested.

C++: protocols::denovo_design::components::CompoundPerturber::add_perturber(class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>) –> void

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber

C++: protocols::denovo_design::components::CompoundPerturber::operator=(const class protocols::denovo_design::components::CompoundPerturber &) –> class protocols::denovo_design::components::CompoundPerturber &

static class_name() str

C++: protocols::denovo_design::components::CompoundPerturber::class_name() –> std::string

clear_perturbers(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) None

Clears list of sub-perturber

C++: protocols::denovo_design::components::CompoundPerturber::clear_perturbers() –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::CompoundPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

static create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::CompoundPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const std::string &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::CompoundPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.CompoundPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_t) None

Sets list of segments that will be ignored by the perturber

C++: protocols::denovo_design::components::CompoundPerturber::set_ignore_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

“mutates” a connection

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber) pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber

C++: protocols::denovo_design::components::ConnectionPerturber::operator=(const class protocols::denovo_design::components::ConnectionPerturber &) –> class protocols::denovo_design::components::ConnectionPerturber &

static class_name() str

C++: protocols::denovo_design::components::ConnectionPerturber::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::ConnectionPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

static create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::ConnectionPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const std::string &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::ConnectionPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_architect(self: pyrosetta.rosetta.protocols.denovo_design.components.ConnectionPerturber, architect: protocols::denovo_design::connection::ConnectionArchitect) None

Sets the architect object that designs the connection to be perturbed

C++: protocols::denovo_design::components::ConnectionPerturber::set_architect(class std::shared_ptr<const class protocols::denovo_design::connection::ConnectionArchitect>) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_t) None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror

Bases: pybind11_builtins.pybind11_object

Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, : pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror) pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror

C++: protocols::denovo_design::components::DivideAndConqueror::operator=(const class protocols::denovo_design::components::DivideAndConqueror &) –> class protocols::denovo_design::components::DivideAndConqueror &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror) pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror

C++: protocols::denovo_design::components::DivideAndConqueror::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::DivideAndConqueror>

divide_and_conquer(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.protocols.denovo_design.components.BuildPhases

C++: protocols::denovo_design::components::DivideAndConqueror::divide_and_conquer(const class protocols::denovo_design::components::StructureData &) const –> class protocols::denovo_design::components::BuildPhases

set_start_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, start_seg_names: pyrosetta.rosetta.std.set_std_string_t) None

C++: protocols::denovo_design::components::DivideAndConqueror::set_start_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

set_stop_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.DivideAndConqueror, stop_seg_names: pyrosetta.rosetta.std.set_std_string_t) None

C++: protocols::denovo_design::components::DivideAndConqueror::set_stop_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold

Bases: pyrosetta.rosetta.utility.excn.Exception

Exception thrown by PoseFolder::apply to indicate folding was not successful

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold, : pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold) pyrosetta.rosetta.protocols.denovo_design.components.EXCN_Fold

C++: protocols::denovo_design::components::EXCN_Fold::operator=(const class protocols::denovo_design::components::EXCN_Fold &) –> class protocols::denovo_design::components::EXCN_Fold &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent

Bases: pyrosetta.rosetta.utility.excn.Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent, : pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent) pyrosetta.rosetta.protocols.denovo_design.components.EXCN_PoseInconsistent

C++: protocols::denovo_design::components::EXCN_PoseInconsistent::operator=(const class protocols::denovo_design::components::EXCN_PoseInconsistent &) –> class protocols::denovo_design::components::EXCN_PoseInconsistent &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent

Bases: pyrosetta.rosetta.utility.excn.Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent, : pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent) pyrosetta.rosetta.protocols.denovo_design.components.EXCN_RemarksNotPresent

C++: protocols::denovo_design::components::EXCN_RemarksNotPresent::operator=(const class protocols::denovo_design::components::EXCN_RemarksNotPresent &) –> class protocols::denovo_design::components::EXCN_RemarksNotPresent &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder, sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::components::ExtendedPoseBuilder::apply(const class protocols::denovo_design::components::StructureData &) const –> class std::shared_ptr<class core::pose::Pose>

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder, : pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder) pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder

C++: protocols::denovo_design::components::ExtendedPoseBuilder::operator=(const class protocols::denovo_design::components::ExtendedPoseBuilder &) –> class protocols::denovo_design::components::ExtendedPoseBuilder &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.ExtendedPoseBuilder) pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder

C++: protocols::denovo_design::components::ExtendedPoseBuilder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseBuilder>

debug(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) bool

Returns whether or not to output debugging PDBs will be outputted which could be useful for fixing problems (true=output extra PDBs; false=don’t output extra PDBs)

C++: protocols::denovo_design::components::PoseBuilder::debug() const –> bool

set_debug(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder, debug: bool) None

Sets whether or not to output debugging PDBs will be outputted which could be useful for fixing problems (true=output extra PDBs; false=don’t output extra PDBs)

C++: protocols::denovo_design::components::PoseBuilder::set_debug(const bool) –> void

write_debug_pdb(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder, pose: pyrosetta.rosetta.core.pose.Pose, filename: str) bool

Writes a debugging pdb (as described above). Does nothing if “debug_” is false and only outputs a PDB if “debug_” is true

C++: protocols::denovo_design::components::PoseBuilder::write_debug_pdb(const class core::pose::Pose &, const std::string &) const –> bool

class pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, : pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph) pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph

C++: protocols::denovo_design::components::FoldGraph::operator=(const class protocols::denovo_design::components::FoldGraph &) –> class protocols::denovo_design::components::FoldGraph &

compute_best_solution(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, staple_loops: pyrosetta.rosetta.std.vector_std_string) pyrosetta.rosetta.utility.vector1_std_set_unsigned_long_t

generates a solution of movable segments to be used in remodel, based on the foldgraph

C++: protocols::denovo_design::components::FoldGraph::compute_best_solution(const class std::vector<std::string, class std::allocator<std::string > > &) const –> class utility::vector1<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::allocator<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > >

create_loops(*args, **kwargs)

Overloaded function.

  1. create_loops(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, staple_loops: pyrosetta.rosetta.std.vector_std_string) -> pyrosetta.rosetta.protocols.loops.Loops

generates a loops object to be used in remodel, based on the foldgraph

C++: protocols::denovo_design::components::FoldGraph::create_loops(const class std::vector<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<class protocols::loops::Loops>

  1. create_loops(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, solution: pyrosetta.rosetta.utility.vector1_std_set_unsigned_long_t) -> pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::denovo_design::components::FoldGraph::create_loops(const class utility::vector1<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::allocator<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > &) const –> class std::shared_ptr<class protocols::loops::Loops>

fold_tree(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, start_segment: pyrosetta.rosetta.std.vector_std_string) pyrosetta.rosetta.core.kinematics.FoldTree

gives a fold tree based on the segments in the given permutation

C++: protocols::denovo_design::components::FoldGraph::fold_tree(const class std::vector<std::string, class std::allocator<std::string > > &) const –> class core::kinematics::FoldTree

nodeidx(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, segment: str) int

given a segment name, returns the associated graph node index

C++: protocols::denovo_design::components::FoldGraph::nodeidx(const std::string &) const –> unsigned long

sd(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph) protocols::denovo_design::components::StructureData

const access to StructureData

C++: protocols::denovo_design::components::FoldGraph::sd() const –> const class protocols::denovo_design::components::StructureData &

segment(self: pyrosetta.rosetta.protocols.denovo_design.components.FoldGraph, nodeidx: int) str

given a node index, returns the associated segment

C++: protocols::denovo_design::components::FoldGraph::segment(const unsigned long) const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing

Bases: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
class PairingType

Bases: pybind11_builtins.pybind11_object

Members:

HELIX

STRAND

HELIX_SHEET

UNKNOWN

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
property name
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
assign(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing, : pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing) pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing

C++: protocols::denovo_design::components::HelixPairing::operator=(const class protocols::denovo_design::components::HelixPairing &) –> class protocols::denovo_design::components::HelixPairing &

static class_name() str

C++: protocols::denovo_design::components::HelixPairing::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::HelixPairing::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static complex_type_name_for_pairing(pairing_name: str) str

C++: protocols::denovo_design::components::SegmentPairing::complex_type_name_for_pairing(const std::string &) –> std::string

static create(type_name: str) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::SegmentPairing::create(const std::string &) –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static get_helix_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_helix_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_hss_triplets(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix-strand-strand triplets in a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_hss_triplets(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all strand pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_strand_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_residue_pairs(sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

Gets pairs of residues involved in strand pairing

C++: protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs(const class protocols::denovo_design::components::StructureData &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

has_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segment: str) bool

C++: protocols::denovo_design::components::SegmentPairing::has_segment(const std::string &) const –> bool

pairing_string(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing, sd: protocols::denovo_design::components::StructureData) str

C++: protocols::denovo_design::components::HelixPairing::pairing_string(const class protocols::denovo_design::components::StructureData &) const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::denovo_design::components::SegmentPairing::parse_my_tag(const class utility::tag::Tag &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::components::HelixPairing::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.std.vector_std_string

C++: protocols::denovo_design::components::SegmentPairing::segments() const –> const class std::vector<std::string, class std::allocator<std::string > > &

set_parallel(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing, parallel: bool) None

Sets whether or not the helices are parallel (true) or antiparallel (false)

C++: protocols::denovo_design::components::HelixPairing::set_parallel(const bool) –> void

set_segments(*args, **kwargs)

Overloaded function.

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments_str: str) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const std::string &) –> void

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments: pyrosetta.rosetta.std.vector_std_string) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType

C++: protocols::denovo_design::components::HelixPairing::type() const –> enum protocols::denovo_design::components::SegmentPairing::PairingType

class pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

“mutates” a helix

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber) pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber

C++: protocols::denovo_design::components::HelixPerturber::operator=(const class protocols::denovo_design::components::HelixPerturber &) –> class protocols::denovo_design::components::HelixPerturber &

static class_name() str

C++: protocols::denovo_design::components::HelixPerturber::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::HelixPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

static create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::HelixPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const std::string &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::HelixPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_architect(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixPerturber, architect: pyrosetta.rosetta.protocols.denovo_design.architects.HelixArchitect) None

Sets the architect object that designs the helix to be perturbed

C++: protocols::denovo_design::components::HelixPerturber::set_architect(class std::shared_ptr<const class protocols::denovo_design::architects::HelixArchitect>) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_t) None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing

Bases: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
class PairingType

Bases: pybind11_builtins.pybind11_object

Members:

HELIX

STRAND

HELIX_SHEET

UNKNOWN

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
property name
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
assign(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing, : pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing) pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing

C++: protocols::denovo_design::components::HelixSheetPairing::operator=(const class protocols::denovo_design::components::HelixSheetPairing &) –> class protocols::denovo_design::components::HelixSheetPairing &

static class_name() str

C++: protocols::denovo_design::components::HelixSheetPairing::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::HelixSheetPairing::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static complex_type_name_for_pairing(pairing_name: str) str

C++: protocols::denovo_design::components::SegmentPairing::complex_type_name_for_pairing(const std::string &) –> std::string

static create(type_name: str) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::SegmentPairing::create(const std::string &) –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static get_helix_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_helix_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_hss_triplets(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix-strand-strand triplets in a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_hss_triplets(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all strand pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_strand_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_residue_pairs(sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

Gets pairs of residues involved in strand pairing

C++: protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs(const class protocols::denovo_design::components::StructureData &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

has_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segment: str) bool

C++: protocols::denovo_design::components::SegmentPairing::has_segment(const std::string &) const –> bool

pairing_string(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing, sd: protocols::denovo_design::components::StructureData) str

C++: protocols::denovo_design::components::HelixSheetPairing::pairing_string(const class protocols::denovo_design::components::StructureData &) const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::denovo_design::components::SegmentPairing::parse_my_tag(const class utility::tag::Tag &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::components::HelixSheetPairing::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.std.vector_std_string

C++: protocols::denovo_design::components::SegmentPairing::segments() const –> const class std::vector<std::string, class std::allocator<std::string > > &

set_segments(*args, **kwargs)

Overloaded function.

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments_str: str) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const std::string &) –> void

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments: pyrosetta.rosetta.std.vector_std_string) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.HelixSheetPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType

C++: protocols::denovo_design::components::HelixSheetPairing::type() const –> enum protocols::denovo_design::components::SegmentPairing::PairingType

class pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator

Bases: pybind11_builtins.pybind11_object

Logic for selection of abego values

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, : pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator) pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator

C++: protocols::denovo_design::components::IdealAbegoGenerator::operator=(const class protocols::denovo_design::components::IdealAbegoGenerator &) –> class protocols::denovo_design::components::IdealAbegoGenerator &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator) pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator

C++: protocols::denovo_design::components::IdealAbegoGenerator::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::IdealAbegoGenerator>

extend_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, secstruct: str) bool

Returns true if the given SS type should be extended or not

C++: protocols::denovo_design::components::IdealAbegoGenerator::extend_ss(const char) const –> bool

retrieve_loop_abegos(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, abego1: str, abego2: str) pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::denovo_design::components::IdealAbegoGenerator::retrieve_loop_abegos(const char, const char) const –> class utility::vector1<std::string, class std::allocator<std::string > >

set_extend_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, extend_ss: str) None
if true, secondary structure may be extended to close the loop. Overall size of the insert

will not change. Therefore, a 4 residue loop might extend a helix by 2 residues and have a 2-residue ideal loop if extend_ss is true. If extend_ss is false, a 4 residue loop must have four loop residues.

C++: protocols::denovo_design::components::IdealAbegoGenerator::set_extend_ss(const std::string &) –> void

set_hh_rules_2021(self: pyrosetta.rosetta.protocols.denovo_design.components.IdealAbegoGenerator, use_hh_rules: bool) None

if true, the connection rules from https://doi.org/10.1101/2021.03.10.434454 will be used.. If false, all possible abego combinations will be sampled

C++: protocols::denovo_design::components::IdealAbegoGenerator::set_hh_rules_2021(const bool) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution

Bases: pyrosetta.rosetta.utility.vector1_std_set_std_string_t

append(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: pyrosetta.rosetta.std.set_std_string_t) None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution, : pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution) pyrosetta.rosetta.protocols.denovo_design.components.NamedSolution

C++: protocols::denovo_design::components::NamedSolution::operator=(const class protocols::denovo_design::components::NamedSolution &) –> class protocols::denovo_design::components::NamedSolution &

back(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) pyrosetta.rosetta.std.set_std_string_t

access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) None

clears the contents

count(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: pyrosetta.rosetta.std.set_std_string_t) int

counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: int) None

erases element at index

extend(othervec)
front(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) pyrosetta.rosetta.std.set_std_string_t

access the first element

l(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) -> pyrosetta.rosetta.std.set_std_string_t

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: int) -> pyrosetta.rosetta.std.set_std_string_t

remove and return item at index

remove(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: pyrosetta.rosetta.std.set_std_string_t) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: int) None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t, arg0: int) None

changes the number of elements stored

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_std_set_std_string_t) int

upper index

class pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions

Bases: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution

append(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, arg0: protocols::denovo_design::components::NamedSolution) None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions, : pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions) pyrosetta.rosetta.protocols.denovo_design.components.NamedSolutions

C++: protocols::denovo_design::components::NamedSolutions::operator=(const class protocols::denovo_design::components::NamedSolutions &) –> class protocols::denovo_design::components::NamedSolutions &

back(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) protocols::denovo_design::components::NamedSolution

access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) None

clears the contents

count(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, arg0: protocols::denovo_design::components::NamedSolution) int

counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, arg0: int) None

erases element at index

extend(othervec)
front(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) protocols::denovo_design::components::NamedSolution

access the first element

l(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) -> protocols::denovo_design::components::NamedSolution

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, arg0: int) -> protocols::denovo_design::components::NamedSolution

remove and return item at index

remove(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, arg0: protocols::denovo_design::components::NamedSolution) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution, arg0: int) None

reserves storage

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_protocols_denovo_design_components_NamedSolution) int

upper index

class pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber

Bases: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

Perturber that does nothing

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber) pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber

C++: protocols::denovo_design::components::NullPerturber::operator=(const class protocols::denovo_design::components::NullPerturber &) –> class protocols::denovo_design::components::NullPerturber &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::NullPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

static create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::NullPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const std::string &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::NullPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_t) None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Folds a pose using random phi/psi torsions

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) None

C++: protocols::denovo_design::components::NullPoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder

C++: protocols::denovo_design::components::NullPoseFolder::operator=(const class protocols::denovo_design::components::NullPoseFolder &) –> class protocols::denovo_design::components::NullPoseFolder &

static class_name() str

C++: protocols::denovo_design::components::NullPoseFolder::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.NullPoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::NullPoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.Picker

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_Picker_t

class used for picking/caching fragments

fragments_for_permutation(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, perm: protocols::denovo_design::components::StructureData, comp_ids: pyrosetta.rosetta.std.list_std_string_t, frag_size: int) pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

picks and caches fragments for the listed components with size frag_size

C++: protocols::denovo_design::components::Picker::fragments_for_permutation(const class protocols::denovo_design::components::StructureData &, const class std::list<std::string, class std::allocator<std::string > > &, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

fragments_for_permutation_take_X_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, perm: protocols::denovo_design::components::StructureData, pose: pyrosetta.rosetta.core.pose.Pose, comp_ids: pyrosetta.rosetta.std.vector_std_string, frag_size: int) pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

picks and caches fragments for the listed components with size frag_size

C++: protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(const class protocols::denovo_design::components::StructureData &, const class core::pose::Pose &, const class std::vector<std::string, class std::allocator<std::string > > &, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

static get_instance() protocols::denovo_design::components::Picker

C++: utility::SingletonBase<protocols::denovo_design::components::Picker>::get_instance() –> class protocols::denovo_design::components::Picker *

pick_and_cache_fragments(*args, **kwargs)

Overloaded function.

  1. pick_and_cache_fragments(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, ss: str, abego: str, loops: pyrosetta.rosetta.protocols.loops.Loops, chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, frag_size: int) -> pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

picks and caches fragments for the given segments with size frag_size

C++: protocols::denovo_design::components::Picker::pick_and_cache_fragments(const std::string &, const std::string &, const class protocols::loops::Loops &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

  1. pick_and_cache_fragments(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, complete_ss: str, complete_abego: pyrosetta.rosetta.utility.vector1_std_string, chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, start_res: int, end_res: int, frag_length: int) -> pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

pick and cache fragments without considering primary sequence

C++: protocols::denovo_design::components::Picker::pick_and_cache_fragments(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const unsigned long, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

  1. pick_and_cache_fragments(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, complete_aa: str, complete_ss: str, complete_abego: pyrosetta.rosetta.utility.vector1_std_string, chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, start_res: int, end_res: int, frag_length: int) -> pyrosetta.rosetta.core.fragment.ConstantLengthFragSet

pick and cache fragments with a primary sequence in mind

C++: protocols::denovo_design::components::Picker::pick_and_cache_fragments(const std::string &, const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, const unsigned long, const unsigned long) –> class std::shared_ptr<class core::fragment::ConstantLengthFragSet>

set_nfrags(self: pyrosetta.rosetta.protocols.denovo_design.components.Picker, nfrags: int) None

C++: protocols::denovo_design::components::Picker::set_nfrags(const unsigned long) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder

Bases: pybind11_builtins.pybind11_object

Builds a pose from StructureData

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder, sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::components::PoseBuilder::apply(const class protocols::denovo_design::components::StructureData &) const –> class std::shared_ptr<class core::pose::Pose>

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder, : pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder

C++: protocols::denovo_design::components::PoseBuilder::operator=(const class protocols::denovo_design::components::PoseBuilder &) –> class protocols::denovo_design::components::PoseBuilder &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder

C++: protocols::denovo_design::components::PoseBuilder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseBuilder>

debug(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder) bool

Returns whether or not to output debugging PDBs will be outputted which could be useful for fixing problems (true=output extra PDBs; false=don’t output extra PDBs)

C++: protocols::denovo_design::components::PoseBuilder::debug() const –> bool

set_debug(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder, debug: bool) None

Sets whether or not to output debugging PDBs will be outputted which could be useful for fixing problems (true=output extra PDBs; false=don’t output extra PDBs)

C++: protocols::denovo_design::components::PoseBuilder::set_debug(const bool) –> void

write_debug_pdb(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseBuilder, pose: pyrosetta.rosetta.core.pose.Pose, filename: str) bool

Writes a debugging pdb (as described above). Does nothing if “debug_” is false and only outputs a PDB if “debug_” is true

C++: protocols::denovo_design::components::PoseBuilder::write_debug_pdb(const class core::pose::Pose &, const std::string &) const –> bool

class pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Bases: pybind11_builtins.pybind11_object

Given a pose with all residues, and a StructureData object, assign a 3D conformation to the pose

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) None

performs folding

  • The pose to be folded, with all residues added. The pose should be prepared with

    any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose should be adjusted, and no residues should be added or removed.

  • Subset of residues for which new backbone conformations will be sampled. Residues

    specified as ‘True’ in movable must also be present in one or more Loops in order to be folded. Movable’s size must match pose.size()

    • Loops to be folded. Cutpoints specified here must be match the cutpoints found in

      the pose. Residues not within any loop should not be folded. Residues contained in a loop but not in the movable set should not be folded.

EXCN_Fold if anything goes wrong in folding. Derived classes should throw this.

C++: protocols::denovo_design::components::PoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::PoseFolder::operator=(const class protocols::denovo_design::components::PoseFolder &) –> class protocols::denovo_design::components::PoseFolder &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::PoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Folds a pose using random phi/psi torsions

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) None

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::operator=(const class protocols::denovo_design::components::RandomTorsionPoseFolder &) –> class protocols::denovo_design::components::RandomTorsionPoseFolder &

static class_name() str

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.RandomTorsionPoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::RandomTorsionPoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder

Bases: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

Folds residues in a pose using RemodelLoopMover

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, pose: pyrosetta.rosetta.core.pose.Pose, movable: pyrosetta.rosetta.utility.vector1_bool, loops: pyrosetta.rosetta.protocols.loops.Loops) None

performs folding

  • The pose to be folded, with all residues added. The pose should be prepared with

    any necessary cutpoints added before giving to the PoseFolder. Torsions in the pose should be adjusted, and no residues should be added or removed.

  • Subset of residues for which new backbone conformations will be sampled. Residues

    specified as ‘True’ in movable must also be present in one or more Loops in order to be folded. Movable’s size must match pose.size()

    • Loops to be folded. Cutpoints specified here must be match the cutpoints found in

      the pose. Residues not within any loop should not be folded. Residues contained in a loop but not in the movable set should not be folded.

EXCN_Fold if anything goes wrong in folding. Derived classes should throw this.

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::apply(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class protocols::loops::Loops &) const –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, : pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::operator=(const class protocols::denovo_design::components::RemodelLoopMoverPoseFolder &) –> class protocols::denovo_design::components::RemodelLoopMoverPoseFolder &

static class_name() str

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder) pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::PoseFolder>

static default_score_function() pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::default_score_function() –> class std::shared_ptr<class core::scoring::ScoreFunction>

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::PoseFolder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

set_scorefxn(*args, **kwargs)

Overloaded function.

  1. set_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

  1. set_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.components.RemodelLoopMoverPoseFolder, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::denovo_design::components::RemodelLoopMoverPoseFolder::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.PoseFolder) str

C++: protocols::denovo_design::components::PoseFolder::type() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals, : pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals

C++: protocols::denovo_design::components::ResidueDihedrals::operator=(const class protocols::denovo_design::components::ResidueDihedrals &) –> class protocols::denovo_design::components::ResidueDihedrals &

lower_phi(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) float

C++: protocols::denovo_design::components::ResidueDihedrals::lower_phi() const –> double

omega(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) float

C++: protocols::denovo_design::components::ResidueDihedrals::omega() const –> double

phi(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) float

C++: protocols::denovo_design::components::ResidueDihedrals::phi() const –> double

psi(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) float

C++: protocols::denovo_design::components::ResidueDihedrals::psi() const –> double

set_in_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals, pose: pyrosetta.rosetta.core.pose.Pose, lower_resid: int) None

C++: protocols::denovo_design::components::ResidueDihedrals::set_in_pose(class core::pose::Pose &, const unsigned long) const –> void

upper_omega(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) float

C++: protocols::denovo_design::components::ResidueDihedrals::upper_omega() const –> double

upper_psi(self: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) float

C++: protocols::denovo_design::components::ResidueDihedrals::upper_psi() const –> double

class pyrosetta.rosetta.protocols.denovo_design.components.Segment

Bases: pybind11_builtins.pybind11_object

manages information about segments of residues

abego(*args, **kwargs)

Overloaded function.

  1. abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) -> str

C++: protocols::denovo_design::components::Segment::abego() const –> const std::string &

  1. abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) -> str

C++: protocols::denovo_design::components::Segment::abego(const long) const –> char

add_lower_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) None

adds “padding” residue before the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::add_lower_padding() –> void

add_upper_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) None

adds “padding” residue after the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::add_upper_padding() –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, : pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.protocols.denovo_design.components.Segment

C++: protocols::denovo_design::components::Segment::operator=(const class protocols::denovo_design::components::Segment &) –> class protocols::denovo_design::components::Segment &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.protocols.denovo_design.components.Segment

C++: protocols::denovo_design::components::Segment::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::Segment>

contains(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, pose_resid: int) bool

C++: protocols::denovo_design::components::Segment::contains(const unsigned long) const –> bool

cterm_included(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

C++: protocols::denovo_design::components::Segment::cterm_included() const –> bool

cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::cutpoint() const –> unsigned long

cutpoint_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

segment residue number for cutpoint

C++: protocols::denovo_design::components::Segment::cutpoint_segment() const –> long

delete_lower_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) None

deletes dummy residues before the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::delete_lower_padding() –> void

delete_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) None

given a segment residue number, delete that residue. Resid for start_local() == 1

C++: protocols::denovo_design::components::Segment::delete_residue(const long) –> void

delete_upper_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) None

deletes dummy residues after the fixed portion of this segment

C++: protocols::denovo_design::components::Segment::delete_upper_padding() –> void

elem_length(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::elem_length() const –> unsigned long

extend(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, secstruct: str, abego: str) None

appends segment by the given secstruct and abego

C++: protocols::denovo_design::components::Segment::extend(const std::string &, const std::string &) –> void

has_free_lower_terminus(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

C++: protocols::denovo_design::components::Segment::has_free_lower_terminus() const –> bool

has_free_upper_terminus(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

C++: protocols::denovo_design::components::Segment::has_free_upper_terminus() const –> bool

has_lower_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

C++: protocols::denovo_design::components::Segment::has_lower_residue() const –> bool

has_template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

returns whether or not this segment contains a template pose

C++: protocols::denovo_design::components::Segment::has_template_pose() const –> bool

has_upper_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

C++: protocols::denovo_design::components::Segment::has_upper_residue() const –> bool

id(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) str

C++: protocols::denovo_design::components::Segment::id() const –> const std::string &

length(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::length() const –> unsigned long

lower(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::lower() const –> unsigned long

lower_dihedrals(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals

C++: protocols::denovo_design::components::Segment::lower_dihedrals() const –> const class protocols::denovo_design::components::ResidueDihedrals &

lower_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

on the chopping block

C++: protocols::denovo_design::components::Segment::lower_local() const –> unsigned long

lower_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::lower_padding() const –> unsigned long

lower_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.core.conformation.Residue

C++: protocols::denovo_design::components::Segment::lower_residue() const –> const class core::conformation::Residue &

lower_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) str

C++: protocols::denovo_design::components::Segment::lower_segment() const –> const std::string &

movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::movable_group() const –> unsigned long

n_residues_after_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

number of residues after the cutpoint, length() if cutpoint not set

C++: protocols::denovo_design::components::Segment::n_residues_after_cutpoint() const –> unsigned long

n_residues_before_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

number of residues before the cutpoint, 0 if cutpoint not set

C++: protocols::denovo_design::components::Segment::n_residues_before_cutpoint() const –> unsigned long

nterm_included(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) bool

C++: protocols::denovo_design::components::Segment::nterm_included() const –> bool

parse_motif(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, motif_str: str) None

construct from motif string (i.e. ‘1LX-10HA-1LA-1LB’)

C++: protocols::denovo_design::components::Segment::parse_motif(const std::string &) –> void

parse_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, tag: pyrosetta.rosetta.utility.tag.Tag) None

construct from xml tag

C++: protocols::denovo_design::components::Segment::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

pose_to_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, pose_resid: int) int
converts a internal segment resid to a pose resid

segment_start - 1 + 1 –> 1 segment_start - 1 + 2 –> 2 segment_start - 1 + N –> N

C++: protocols::denovo_design::components::Segment::pose_to_segment(const unsigned long) const –> long

safe(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::safe() const –> unsigned long

safe_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

segment residue number for “safe” residue

C++: protocols::denovo_design::components::Segment::safe_segment() const –> long

segment_to_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) int

converts a segment resid to a “local” resid

C++: protocols::denovo_design::components::Segment::segment_to_local(const long) const –> unsigned long

segment_to_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) int
converts a internal segment resid to a pose resid

1 –> segment_start - 1 + 1 2 –> segment_start - 1 + 2 N –> segment_start - 1 + N

C++: protocols::denovo_design::components::Segment::segment_to_pose(const long) const –> unsigned long

set_abego(*args, **kwargs)

Overloaded function.

  1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, abego_str: str) -> None

C++: protocols::denovo_design::components::Segment::set_abego(const std::string &) –> void

  1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, abego: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::denovo_design::components::Segment::set_abego(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_cterm_included(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, inc: bool) None

Sets whether the n-terminal residue of the segment is a part of the segment (or whether it is “padding”)

C++: protocols::denovo_design::components::Segment::set_cterm_included(const bool) –> void

set_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) None
sets cutpoint for this segment to be the ith residue in the segment

cut = segment_start - 1 + cut_res

C++: protocols::denovo_design::components::Segment::set_cutpoint(const long) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, id_val: str) None

C++: protocols::denovo_design::components::Segment::set_id(const std::string &) –> void

set_lower_dihedrals(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, dih: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) None

C++: protocols::denovo_design::components::Segment::set_lower_dihedrals(const class protocols::denovo_design::components::ResidueDihedrals &) –> void

set_lower_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, rsd: pyrosetta.rosetta.core.conformation.Residue) None

C++: protocols::denovo_design::components::Segment::set_lower_residue(class std::shared_ptr<const class core::conformation::Residue>) –> void

set_lower_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, comp: str) None

C++: protocols::denovo_design::components::Segment::set_lower_segment(const std::string &) –> void

set_movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, mg: int) None

C++: protocols::denovo_design::components::Segment::set_movable_group(const unsigned long) –> void

set_nterm_included(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, inc: bool) None

Sets whether the n-terminal residue of the segment is a part of the segment (or whether it is “padding”)

C++: protocols::denovo_design::components::Segment::set_nterm_included(const bool) –> void

set_pose_start(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, pose_resid: int) None

C++: protocols::denovo_design::components::Segment::set_pose_start(const unsigned long) –> void

set_safe(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int) None
sets safe residue for this segment to be the ith residue in the segment

safe = segment_start - 1 + cut_res

C++: protocols::denovo_design::components::Segment::set_safe(const long) –> void

set_ss(*args, **kwargs)

Overloaded function.

  1. set_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, segment_resid: int, ss_type: str) -> None

C++: protocols::denovo_design::components::Segment::set_ss(const long, char) –> void

  1. set_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, secstruct: str) -> None

C++: protocols::denovo_design::components::Segment::set_ss(const std::string &) –> void

set_template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, template_pose: pyrosetta.rosetta.core.pose.Pose, start_resid: int, stop_resid: int) None

sets template pose to be the given residues from template_pose

C++: protocols::denovo_design::components::Segment::set_template_pose(const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

set_upper_dihedrals(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, dih: pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals) None

C++: protocols::denovo_design::components::Segment::set_upper_dihedrals(const class protocols::denovo_design::components::ResidueDihedrals &) –> void

set_upper_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, rsd: pyrosetta.rosetta.core.conformation.Residue) None

C++: protocols::denovo_design::components::Segment::set_upper_residue(class std::shared_ptr<const class core::conformation::Residue>) –> void

set_upper_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment, comp: str) None

C++: protocols::denovo_design::components::Segment::set_upper_segment(const std::string &) –> void

ss(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) str

C++: protocols::denovo_design::components::Segment::ss() const –> const std::string &

start(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::start() const –> unsigned long

start_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::start_local() const –> unsigned long

stop(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::stop() const –> unsigned long

stop_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::stop_local() const –> unsigned long

template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.core.pose.Pose

returns template pose

C++: protocols::denovo_design::components::Segment::template_pose() const –> class std::shared_ptr<const class core::pose::Pose>

upper(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::upper() const –> unsigned long

upper_dihedrals(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.protocols.denovo_design.components.ResidueDihedrals

C++: protocols::denovo_design::components::Segment::upper_dihedrals() const –> const class protocols::denovo_design::components::ResidueDihedrals &

upper_local(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::upper_local() const –> unsigned long

upper_padding(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) int

C++: protocols::denovo_design::components::Segment::upper_padding() const –> unsigned long

upper_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) pyrosetta.rosetta.core.conformation.Residue

C++: protocols::denovo_design::components::Segment::upper_residue() const –> const class core::conformation::Residue &

upper_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.Segment) str

C++: protocols::denovo_design::components::Segment::upper_segment() const –> const std::string &

class pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts

Bases: pybind11_builtins.pybind11_object

HELIX = <SegmentType.HELIX: 1>
LIGAND = <SegmentType.LIGAND: 4>
LOOP = <SegmentType.LOOP: 3>
NUM_SEGMENT_TYPES = <SegmentType.NUM_SEGMENT_TYPES: 5>
STRAND = <SegmentType.STRAND: 2>
class SegmentType

Bases: pybind11_builtins.pybind11_object

Members:

HELIX

STRAND

LOOP

LIGAND

NUM_SEGMENT_TYPES

HELIX = <SegmentType.HELIX: 1>
LIGAND = <SegmentType.LIGAND: 4>
LOOP = <SegmentType.LOOP: 3>
NUM_SEGMENT_TYPES = <SegmentType.NUM_SEGMENT_TYPES: 5>
STRAND = <SegmentType.STRAND: 2>
property name
new_segment_name(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts, ss_type: str, seqpos: int) str

C++: protocols::denovo_design::components::SegmentCounts::new_segment_name(const char, const unsigned long) –> std::string

class pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet

Bases: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t

add(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, arg0: Tuple[str, str]) None
assign(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet, : pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet

C++: protocols::denovo_design::components::SegmentPairSet::operator=(const class protocols::denovo_design::components::SegmentPairSet &) –> class protocols::denovo_design::components::SegmentPairSet &

clear(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) None

C++: std::set<std::pair<std::string, std::string >>::clear() –> void

count(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, __x: Tuple[str, str]) int

C++: std::set<std::pair<std::string, std::string >>::count(const struct std::pair<std::string, std::string > &) const –> unsigned long

discard(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, arg0: Tuple[str, str]) None

discard element

empty(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) bool

C++: std::set<std::pair<std::string, std::string >>::empty() const –> bool

equal_range(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, __x: Tuple[str, str]) Tuple[std::_Rb_tree_const_iterator<std::pair<std::string, std::string> >, std::_Rb_tree_const_iterator<std::pair<std::string, std::string> >]

C++: std::set<std::pair<std::string, std::string >>::equal_range(const struct std::pair<std::string, std::string > &) –> struct std::pair<struct std::_Rb_tree_const_iterator<struct std::pair<std::string, std::string > >, struct std::_Rb_tree_const_iterator<struct std::pair<std::string, std::string > > >

erase(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, __x: Tuple[str, str]) int

C++: std::set<std::pair<std::string, std::string >>::erase(const struct std::pair<std::string, std::string > &) –> unsigned long

get_allocator(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) std::allocator<std::pair<std::string, std::string> >

C++: std::set<std::pair<std::string, std::string >>::get_allocator() const –> class std::allocator<struct std::pair<std::string, std::string > >

insert(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, __x: Tuple[str, str]) Tuple[std::_Rb_tree_const_iterator<std::pair<std::string, std::string> >, bool]

C++: std::set<std::pair<std::string, std::string >>::insert(const struct std::pair<std::string, std::string > &) –> struct std::pair<struct std::_Rb_tree_const_iterator<struct std::pair<std::string, std::string > >, bool>

key_comp(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) std::less<std::pair<std::string, std::string> >

C++: std::set<std::pair<std::string, std::string >>::key_comp() const –> struct std::less<struct std::pair<std::string, std::string > >

max_size(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) int

C++: std::set<std::pair<std::string, std::string >>::max_size() const –> unsigned long

segment_name_set(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairSet) pyrosetta.rosetta.std.set_std_string_t

C++: protocols::denovo_design::components::SegmentPairSet::segment_name_set() const –> class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > >

size(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) int

C++: std::set<std::pair<std::string, std::string >>::size() const –> unsigned long

swap(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t, __x: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) None

C++: std::set<std::pair<std::string, std::string >>::swap(class std::set<struct std::pair<std::string, std::string >, struct std::less<struct std::pair<std::string, std::string > >, class std::allocator<struct std::pair<std::string, std::string > > > &) –> void

value_comp(self: pyrosetta.rosetta.std.set_std_pair_std_string_std_string_t) std::less<std::pair<std::string, std::string> >

C++: std::set<std::pair<std::string, std::string >>::value_comp() const –> struct std::less<struct std::pair<std::string, std::string > >

class pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

Bases: pybind11_builtins.pybind11_object

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
class PairingType

Bases: pybind11_builtins.pybind11_object

Members:

HELIX

STRAND

HELIX_SHEET

UNKNOWN

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
property name
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
assign(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, : pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::SegmentPairing::operator=(const class protocols::denovo_design::components::SegmentPairing &) –> class protocols::denovo_design::components::SegmentPairing &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::SegmentPairing::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static complex_type_name_for_pairing(pairing_name: str) str

C++: protocols::denovo_design::components::SegmentPairing::complex_type_name_for_pairing(const std::string &) –> std::string

static create(type_name: str) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::SegmentPairing::create(const std::string &) –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static get_helix_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_helix_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_hss_triplets(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix-strand-strand triplets in a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_hss_triplets(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all strand pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_strand_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_residue_pairs(sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

Gets pairs of residues involved in strand pairing

C++: protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs(const class protocols::denovo_design::components::StructureData &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

has_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segment: str) bool

C++: protocols::denovo_design::components::SegmentPairing::has_segment(const std::string &) const –> bool

pairing_string(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, sd: protocols::denovo_design::components::StructureData) str

C++: protocols::denovo_design::components::SegmentPairing::pairing_string(const class protocols::denovo_design::components::StructureData &) const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::denovo_design::components::SegmentPairing::parse_my_tag(const class utility::tag::Tag &) –> void

segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.std.vector_std_string

C++: protocols::denovo_design::components::SegmentPairing::segments() const –> const class std::vector<std::string, class std::allocator<std::string > > &

set_segments(*args, **kwargs)

Overloaded function.

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments_str: str) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const std::string &) –> void

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments: pyrosetta.rosetta.std.vector_std_string) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

type(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType

C++: protocols::denovo_design::components::SegmentPairing::type() const –> enum protocols::denovo_design::components::SegmentPairing::PairingType

class pyrosetta.rosetta.protocols.denovo_design.components.SheetDB

Bases: pybind11_builtins.pybind11_object

class used to create/manipulate a database of sheets using a list of pdb files

add_sheet(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, pose: pyrosetta.rosetta.core.pose.Pose, nstrands: int, orientations: str, lengths_shifts: str, check_descriptor_against_pose: bool) None

add a sheet to the database

C++: protocols::denovo_design::components::SheetDB::add_sheet(class std::shared_ptr<class core::pose::Pose>, const unsigned long, const std::string &, const std::string &, const bool) –> void

add_sheets_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, pose: pyrosetta.rosetta.core.pose.Pose) int

adds sheet(s) based on a pose – returns # of sheets added

C++: protocols::denovo_design::components::SheetDB::add_sheets_from_pose(class core::pose::Pose &) –> int

add_sheets_from_spairs(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, pose: pyrosetta.rosetta.core.pose.Pose, spairs: protocols::fldsgn::topology::StrandPairingSet, ss_info: protocols::fldsgn::topology::SS_Info2) int

adds sheet(s) based on a strand pairing set and pose – returns # of sheets added

C++: protocols::denovo_design::components::SheetDB::add_sheets_from_spairs(const class core::pose::Pose &, class protocols::fldsgn::topology::StrandPairingSet &, const class protocols::fldsgn::topology::SS_Info2 &) –> int

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, : pyrosetta.rosetta.protocols.denovo_design.components.SheetDB) pyrosetta.rosetta.protocols.denovo_design.components.SheetDB

C++: protocols::denovo_design::components::SheetDB::operator=(const class protocols::denovo_design::components::SheetDB &) –> class protocols::denovo_design::components::SheetDB &

lengths_shifts(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, nstrands: int, orientations: str) pyrosetta.rosetta.utility.vector1_std_string

queries the database for all lengths/shifts with nstrands strands and given orientations

C++: protocols::denovo_design::components::SheetDB::lengths_shifts(const unsigned long, const std::string &) const –> class utility::vector1<std::string, class std::allocator<std::string > >

nstrand_values(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB) pyrosetta.rosetta.utility.vector1_unsigned_long

queries the database for all strand lengths

C++: protocols::denovo_design::components::SheetDB::nstrand_values() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

orientations(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, nstrands: int) pyrosetta.rosetta.utility.vector1_std_string

queries the database for all orientations with nstrands strands

C++: protocols::denovo_design::components::SheetDB::orientations(const unsigned long) const –> class utility::vector1<std::string, class std::allocator<std::string > >

set_db_path(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, db_path: str) None

set location of sheet database files

C++: protocols::denovo_design::components::SheetDB::set_db_path(const std::string &) –> void

set_idealize(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, idealize_val: bool) None

C++: protocols::denovo_design::components::SheetDB::set_idealize(const bool) –> void

set_sheetlist(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, nstrands: int, in_orientations: str, in_lengths: str) None

add a sheet to the database

C++: protocols::denovo_design::components::SheetDB::set_sheetlist(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const unsigned long, const std::string &, const std::string &) –> void

set_sheetlist_as_is(self: pyrosetta.rosetta.protocols.denovo_design.components.SheetDB, list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t, nstrands: int, orientations: str, lengths: str) None

adds a sheet list as it is presented

C++: protocols::denovo_design::components::SheetDB::set_sheetlist_as_is(const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &, const unsigned long, const std::string &, const std::string &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.SolutionPredicate

Bases: pybind11_builtins.pybind11_object

class pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation

Bases: pybind11_builtins.pybind11_object

Individual strands are oriented pointing either “UP” or “DOWN”

If two adjacent strands have the same orientation, they are parallel If two adjacent strands have different orientation, they are antiparallel

Members:

UP

DOWN

ORIENTATIONS_END

DOWN = <StrandOrientation.DOWN: 2>
ORIENTATIONS_END = <StrandOrientation.ORIENTATIONS_END: 3>
UP = <StrandOrientation.UP: 1>
property name
class pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing

Bases: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
class PairingType

Bases: pybind11_builtins.pybind11_object

Members:

HELIX

STRAND

HELIX_SHEET

UNKNOWN

HELIX = <PairingType.HELIX: 1>
HELIX_SHEET = <PairingType.HELIX_SHEET: 3>
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
property name
STRAND = <PairingType.STRAND: 2>
UNKNOWN = <PairingType.UNKNOWN: 4>
assign(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing, : pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing

C++: protocols::denovo_design::components::StrandPairing::operator=(const class protocols::denovo_design::components::StrandPairing &) –> class protocols::denovo_design::components::StrandPairing &

static class_name() str

C++: protocols::denovo_design::components::StrandPairing::class_name() –> std::string

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::StrandPairing::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static complex_type_name_for_pairing(pairing_name: str) str

C++: protocols::denovo_design::components::SegmentPairing::complex_type_name_for_pairing(const std::string &) –> std::string

static create(type_name: str) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::SegmentPairing::create(const std::string &) –> class std::shared_ptr<class protocols::denovo_design::components::SegmentPairing>

static get_helix_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_helix_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_hss_triplets(sd: protocols::denovo_design::components::StructureData) str

Gets string for all helix-strand-strand triplets in a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_hss_triplets(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_pairings(sd: protocols::denovo_design::components::StructureData) str

Gets string for all strand pairings from a StructureData

C++: protocols::denovo_design::components::SegmentPairing::get_strand_pairings(const class protocols::denovo_design::components::StructureData &) –> std::string

static get_strand_residue_pairs(sd: protocols::denovo_design::components::StructureData) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

Gets pairs of residues involved in strand pairing

C++: protocols::denovo_design::components::SegmentPairing::get_strand_residue_pairs(const class protocols::denovo_design::components::StructureData &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

has_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segment: str) bool

C++: protocols::denovo_design::components::SegmentPairing::has_segment(const std::string &) const –> bool

orient1(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation

C++: protocols::denovo_design::components::StrandPairing::orient1() const –> enum protocols::denovo_design::components::StrandOrientation

orient2(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation

C++: protocols::denovo_design::components::StrandPairing::orient2() const –> enum protocols::denovo_design::components::StrandOrientation

pairing_string(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing, sd: protocols::denovo_design::components::StructureData) str

C++: protocols::denovo_design::components::StrandPairing::pairing_string(const class protocols::denovo_design::components::StructureData &) const –> std::string

parallel(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) bool

C++: protocols::denovo_design::components::StrandPairing::parallel() const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, tag: pyrosetta.rosetta.utility.tag.Tag) None

C++: protocols::denovo_design::components::SegmentPairing::parse_my_tag(const class utility::tag::Tag &) –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::denovo_design::components::StrandPairing::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) pyrosetta.rosetta.std.vector_std_string

C++: protocols::denovo_design::components::SegmentPairing::segments() const –> const class std::vector<std::string, class std::allocator<std::string > > &

set_orient1(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing, orient: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) None

Sets the orientation for the first strand; used to determine whether the strands are parallel or antiparallel

C++: protocols::denovo_design::components::StrandPairing::set_orient1(const enum protocols::denovo_design::components::StrandOrientation) –> void

set_orient2(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing, orient: pyrosetta.rosetta.protocols.denovo_design.components.StrandOrientation) None

Sets the orientation for the second strand; used to determine whether the strands are parallel or antiparallel

C++: protocols::denovo_design::components::StrandPairing::set_orient2(const enum protocols::denovo_design::components::StrandOrientation) –> void

set_segments(*args, **kwargs)

Overloaded function.

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments_str: str) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const std::string &) –> void

  1. set_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing, segments: pyrosetta.rosetta.std.vector_std_string) -> None

C++: protocols::denovo_design::components::SegmentPairing::set_segments(const class std::vector<std::string, class std::allocator<std::string > > &) –> void

set_shift(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing, shift: int) None

Sets the register shift

C++: protocols::denovo_design::components::StrandPairing::set_shift(const long) –> void

shift(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) int

C++: protocols::denovo_design::components::StrandPairing::shift() const –> long

type(self: pyrosetta.rosetta.protocols.denovo_design.components.StrandPairing) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing.PairingType

C++: protocols::denovo_design::components::StrandPairing::type() const –> enum protocols::denovo_design::components::SegmentPairing::PairingType

class pyrosetta.rosetta.protocols.denovo_design.components.StructureData

Bases: pyrosetta.rosetta.basic.datacache.WriteableCacheableData

abego(*args, **kwargs)

Overloaded function.

  1. abego(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) -> str

return abego string

C++: protocols::denovo_design::components::StructureData::abego() const –> const std::string &

  1. abego(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid: int) -> str

abego of residue resid

C++: protocols::denovo_design::components::StructureData::abego(const unsigned long) const –> char

add_covalent_bond(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, res1: int, atom1: str, res2: int, atom2: str) None

C++: protocols::denovo_design::components::StructureData::add_covalent_bond(const unsigned long, const std::string &, const unsigned long, const std::string &) –> void

add_pairing(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, pairing: pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing) None

C++: protocols::denovo_design::components::StructureData::add_pairing(const class protocols::denovo_design::components::SegmentPairing &) –> void

add_prefix_to_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, prefix: str) None

renames a residue segment and updates all connections

C++: protocols::denovo_design::components::StructureData::add_prefix_to_segments(const std::string &) –> void

add_segment(*args, **kwargs)

Overloaded function.

  1. add_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resis: pyrosetta.rosetta.protocols.denovo_design.components.Segment) -> None

adds a residues segment to the end of the list

C++: protocols::denovo_design::components::StructureData::add_segment(const class protocols::denovo_design::components::Segment &) –> void

  1. add_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resis: pyrosetta.rosetta.protocols.denovo_design.components.Segment, insert_before_segment: str) -> None

adds a residues segment – will be ordered before the given segment

C++: protocols::denovo_design::components::StructureData::add_segment(const class protocols::denovo_design::components::Segment &, const std::string &) –> void

alias(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, alias: str) int

given a residue alias, returns a pose residue number

C++: protocols::denovo_design::components::StructureData::alias(const std::string &) const –> unsigned long

aliases(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.std.map_std_string_protocols_denovo_design_components_Alias

gets all alias data

C++: protocols::denovo_design::components::StructureData::aliases() const –> const class std::map<std::string, class protocols::denovo_design::components::Alias, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class protocols::denovo_design::components::Alias> > > &

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, : pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.protocols.denovo_design.components.StructureData

C++: protocols::denovo_design::components::StructureData::operator=(const class protocols::denovo_design::components::StructureData &) –> class protocols::denovo_design::components::StructureData &

available_lower_termini(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.std.vector_std_string

returns segments which have free lower termini

C++: protocols::denovo_design::components::StructureData::available_lower_termini() const –> class std::vector<std::string, class std::allocator<std::string > >

available_upper_termini(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.std.vector_std_string

returns segments which have free upper termini

C++: protocols::denovo_design::components::StructureData::available_upper_termini() const –> class std::vector<std::string, class std::allocator<std::string > >

check_consistency(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

checks consistency of the data

EXCN_PoseInconsistent if there is a problem

C++: protocols::denovo_design::components::StructureData::check_consistency() const –> void

check_pose_consistency(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, pose: pyrosetta.rosetta.core.pose.Pose) None

checks the permutation for internal consistency vs a pose

EXCN_PoseInconsistent if there is a problem

C++: protocols::denovo_design::components::StructureData::check_pose_consistency(const class core::pose::Pose &) const –> void

choose_new_movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) int

chooses a new movable group which doesn’t conflict with existing ones

C++: protocols::denovo_design::components::StructureData::choose_new_movable_group() const –> unsigned long

static class_name() str

C++: protocols::denovo_design::components::StructureData::class_name() –> std::string

clear_pairings(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

C++: protocols::denovo_design::components::StructureData::clear_pairings() –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::denovo_design::components::StructureData::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

connect_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment1: str, segment2: str) None

connects the given chains together, doesn’t update anything – don’t call this on its own unless you know what you’re doing

C++: protocols::denovo_design::components::StructureData::connect_segments(const std::string &, const std::string &) –> void

connected_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg: str, stop_at_cutpoint: bool) pyrosetta.rosetta.std.list_std_string_t

returns an ordered list of segments which are all connected containing seg

  • if true, segments past a cutpoint will not be counted as connected

C++: protocols::denovo_design::components::StructureData::connected_segments(const std::string &, const bool) const –> class std::list<std::string, class std::allocator<std::string > >

copy_data(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, perm: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

copies user data fields from one permutation to this one – overwrites existing data

C++: protocols::denovo_design::components::StructureData::copy_data(const class protocols::denovo_design::components::StructureData &) –> void

cutpoints(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_unsigned_long

returns list of all cutpoints, in N–>C order

C++: protocols::denovo_design::components::StructureData::cutpoints() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

data_int(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.std.map_std_string_int

gets all real number data

C++: protocols::denovo_design::components::StructureData::data_int() const –> const class std::map<std::string, int, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, int> > > &

data_real(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.std.map_std_string_double

gets all real number data

C++: protocols::denovo_design::components::StructureData::data_real() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

data_str(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.std.map_std_string_std_string

gets all string data

C++: protocols::denovo_design::components::StructureData::data_str() const –> const class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

datatype(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) str

C++: protocols::denovo_design::components::StructureData::datatype() const –> std::string

declare_covalent_bond(*args, **kwargs)

Overloaded function.

  1. declare_covalent_bond(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg1: str, res1: int, atom1: str, seg2: str, res2: int, atom2: str) -> None

declares a covalent bond between the specified atoms

C++: protocols::denovo_design::components::StructureData::declare_covalent_bond(const std::string &, const unsigned long, const std::string &, const std::string &, const unsigned long, const std::string &) –> void

  1. declare_covalent_bond(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, res1: int, atom1: str, res2: int, atom2: str) -> None

declares a covalent bond using pose residues

C++: protocols::denovo_design::components::StructureData::declare_covalent_bond(const unsigned long, const std::string &, const unsigned long, const std::string &) –> void

delete_jump_and_intervening_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment1: str, segment2: str) None

removes jump and cutpoint between the two segments to create a single polymer chain

C++: protocols::denovo_design::components::StructureData::delete_jump_and_intervening_cutpoint(const std::string &, const std::string &) –> void

delete_leading_residues(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg: str) None

deletes the residues between the segment N terminus and the N anchor point

C++: protocols::denovo_design::components::StructureData::delete_leading_residues(const std::string &) –> void

delete_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, pose_resid: int) None

C++: protocols::denovo_design::components::StructureData::delete_residue(const unsigned long) –> void

delete_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment: str) None

removes all traces of the given segment from the object

C++: protocols::denovo_design::components::StructureData::delete_segment(const std::string &) –> void

delete_trailing_residues(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg: str) None

deletes the residues between the segment C terminus and the C anchor point

C++: protocols::denovo_design::components::StructureData::delete_trailing_residues(const std::string &) –> void

disconnect_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment1: str, segment2: str) None

connects the given chains together, doesn’t update anything – don’t call this on its own unless you know what you’re doing

C++: protocols::denovo_design::components::StructureData::disconnect_segments(const std::string &, const std::string &) –> void

get_data_int(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str) int

gets integer data

C++: protocols::denovo_design::components::StructureData::get_data_int(const std::string &, const std::string &) const –> int

get_data_real(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str) float

gets real number data

C++: protocols::denovo_design::components::StructureData::get_data_real(const std::string &, const std::string &) const –> double

get_data_str(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str) str

gets real number data

C++: protocols::denovo_design::components::StructureData::get_data_str(const std::string &, const std::string &) const –> const std::string &

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

has_alias(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, alias: str) bool

given a residue alias, returns a pose residue number

C++: protocols::denovo_design::components::StructureData::has_alias(const std::string &) const –> bool

has_data_int(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str) bool

check for integer data

C++: protocols::denovo_design::components::StructureData::has_data_int(const std::string &, const std::string &) const –> bool

has_data_real(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str) bool

check for real number data

C++: protocols::denovo_design::components::StructureData::has_data_real(const std::string &, const std::string &) const –> bool

has_data_str(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str) bool

gets real number data

C++: protocols::denovo_design::components::StructureData::has_data_str(const std::string &, const std::string &) const –> bool

has_free_lower_terminus(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id_val: str) bool

tells if the segment given has an available lower terminus

C++: protocols::denovo_design::components::StructureData::has_free_lower_terminus(const std::string &) const –> bool

has_free_upper_terminus(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id_val: str) bool

tells if the segment given has an available lower terminus

C++: protocols::denovo_design::components::StructureData::has_free_upper_terminus(const std::string &) const –> bool

has_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg: str) bool

true if this permutation contains a residue segment named seg

C++: protocols::denovo_design::components::StructureData::has_segment(const std::string &) const –> bool

has_segment_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, sname: str) bool

returns true if this object has a group of segments with the given name

C++: protocols::denovo_design::components::StructureData::has_segment_group(const std::string &) const –> bool

id(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) str

returns the id of this permutation

C++: protocols::denovo_design::components::StructureData::id() const –> const std::string &

length(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) int

returns the length of this permutation

C++: protocols::denovo_design::components::StructureData::length() const –> unsigned long

lower_anchor(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id_val: str) int

returns n-terminal residue of the chain represented by given string

C++: protocols::denovo_design::components::StructureData::lower_anchor(const std::string &) const –> unsigned long

mark_connected(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, lower_seg: str, upper_seg: str) None

marks the given segments as covanlently connected

C++: protocols::denovo_design::components::StructureData::mark_connected(const std::string &, const std::string &) –> void

mark_disconnected(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg1: str, seg2: str) None

unmarks the given segments as covalently connected

C++: protocols::denovo_design::components::StructureData::mark_disconnected(const std::string &, const std::string &) –> void

merge(*args, **kwargs)

Overloaded function.

  1. merge(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, other: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) -> None

merge all data and segments from “other” into this StructureData

C++: protocols::denovo_design::components::StructureData::merge(const class protocols::denovo_design::components::StructureData &) –> void

  1. merge(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, other: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segments: pyrosetta.rosetta.std.vector_std_string) -> None

merge given data and segments from “other” into this StructureData

C++: protocols::denovo_design::components::StructureData::merge(const class protocols::denovo_design::components::StructureData &, const class std::vector<std::string, class std::allocator<std::string > > &) –> void

merge_before(*args, **kwargs)

Overloaded function.

  1. merge_before(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, other: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, position: str) -> None

merge all data and segments from “other” into this StructureData before the given position

C++: protocols::denovo_design::components::StructureData::merge_before(const class protocols::denovo_design::components::StructureData &, const std::string &) –> void

  1. merge_before(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, other: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, position: str, segments: pyrosetta.rosetta.std.vector_std_string) -> None

merge all data and given segments from “other” into this StructureData before the given position

C++: protocols::denovo_design::components::StructureData::merge_before(const class protocols::denovo_design::components::StructureData &, const std::string &, const class std::vector<std::string, class std::allocator<std::string > > &) –> void

merge_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment1: str, segment2: str, new_name: str) None

merges two segments into one that has the name new_name. They must be next to each other in sequence.

C++: protocols::denovo_design::components::StructureData::merge_segments(const std::string &, const std::string &, const std::string &) –> void

movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid: int) int

movable group of segment which contains residue resid

C++: protocols::denovo_design::components::StructureData::movable_group(const unsigned long) const –> unsigned long

movable_groups(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_unsigned_long

computes and returns a set of movable groups

C++: protocols::denovo_design::components::StructureData::movable_groups() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

move_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment1: str, segment2: str) None

re-arranges segments suchs that segment2 follows segment1 in sequence

C++: protocols::denovo_design::components::StructureData::move_segment(const std::string &, const std::string &) –> void

non_polymer_bond(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg1: str, seg2: str) pyrosetta.rosetta.protocols.denovo_design.components.BondInfo

finds a non-peptide bond between two segments, returns end() if there isn’t one

C++: protocols::denovo_design::components::StructureData::non_polymer_bond(const std::string &, const std::string &) const –> const class protocols::denovo_design::components::BondInfo &

non_polymer_bond_exists(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg1: str, seg2: str) bool

tells whether a non-polymer bond exists between the given segments

C++: protocols::denovo_design::components::StructureData::non_polymer_bond_exists(const std::string &, const std::string &) const –> bool

num_chains(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) int

Total number of chains WARNING: This is an O(n) operation, where n is number of residue segments

C++: protocols::denovo_design::components::StructureData::num_chains() const –> unsigned long

pairing(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segments: pyrosetta.rosetta.std.vector_std_string) pyrosetta.rosetta.protocols.denovo_design.components.SegmentPairing

C++: protocols::denovo_design::components::StructureData::pairing(const class std::vector<std::string, class std::allocator<std::string > > &) const –> class std::shared_ptr<const class protocols::denovo_design::components::SegmentPairing>

parse_subtag(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, tag: pyrosetta.rosetta.utility.tag.Tag) None

Retrieves data from an XML subtag

C++: protocols::denovo_design::components::StructureData::parse_subtag(class std::shared_ptr<const class utility::tag::Tag>) –> void

parse_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, tag: pyrosetta.rosetta.utility.tag.Tag) None

Retrieves data from an XML tag

C++: protocols::denovo_design::components::StructureData::parse_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

pose_length(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) int

returns the total length of this permutation, including n-, c-terminal loop residues which are basically for show

C++: protocols::denovo_design::components::StructureData::pose_length() const –> unsigned long

pose_residue(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_name: str, local_res: int) int

returns the actual residue number of the given name and res #

C++: protocols::denovo_design::components::StructureData::pose_residue(const std::string &, const unsigned long) const –> unsigned long

rename_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, old_name: str, new_name: str) None

renames a residue segment and updates all connections

C++: protocols::denovo_design::components::StructureData::rename_segment(const std::string &, const std::string &) –> void

renumber_movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, oldg: int, newg: int) None

renumbers movable group “oldg” to have new number “newg”

C++: protocols::denovo_design::components::StructureData::renumber_movable_group(const unsigned long, const unsigned long) –> void

replace_segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg_name: str, segment: pyrosetta.rosetta.protocols.denovo_design.components.Segment) None

replace segment named seg_name with the given new segment

C++: protocols::denovo_design::components::StructureData::replace_segment(const std::string &, const class protocols::denovo_design::components::Segment &) –> void

retrieve_remarks(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.io.Remarks

retrieves saved remarks, makes any enzdes residues specific to the given pose

C++: protocols::denovo_design::components::StructureData::retrieve_remarks(const class core::pose::Pose &) const –> class core::io::Remarks

save_remarks(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, remarks: pyrosetta.rosetta.core.io.Remarks) None

Saves given remarks changes enzdes residues to generic segment name/number

C++: protocols::denovo_design::components::StructureData::save_remarks(const class core::io::Remarks &) –> void

segment(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id_val: str) pyrosetta.rosetta.protocols.denovo_design.components.Segment

returns segment represented by given string

C++: protocols::denovo_design::components::StructureData::segment(const std::string &) const –> const class protocols::denovo_design::components::Segment &

segment_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, sname: str) pyrosetta.rosetta.std.vector_std_string

returns true if this object has a group of segments with the given name

C++: protocols::denovo_design::components::StructureData::segment_group(const std::string &) const –> class std::vector<std::string, class std::allocator<std::string > >

segment_name(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, res: int) str

returns segment which includes residue number res

C++: protocols::denovo_design::components::StructureData::segment_name(const unsigned long) const –> const std::string &

segments_in_movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, group: int) pyrosetta.rosetta.std.vector_std_string

computes and returns a set of segments which are in the given movable group

C++: protocols::denovo_design::components::StructureData::segments_in_movable_group(const unsigned long) const –> class std::vector<std::string, class std::allocator<std::string > >

set_abego(*args, **kwargs)

Overloaded function.

  1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, abego: str) -> None

Set abego to use for the entire pose/all segments using a string

C++: protocols::denovo_design::components::StructureData::set_abego(const std::string &) –> void

  1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, abego: pyrosetta.rosetta.utility.vector1_std_string) -> None

Set abego to use for the entire pose/all segments using a vector of one-character strings

C++: protocols::denovo_design::components::StructureData::set_abego(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

  1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment: str, abego: str) -> None

Set abego to use for a specific segment using a string

C++: protocols::denovo_design::components::StructureData::set_abego(const std::string &, const std::string &) –> void

  1. set_abego(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment: str, abego: pyrosetta.rosetta.utility.vector1_std_string) -> None

Set abego to use for a specific segment using a vector of one-character strings

C++: protocols::denovo_design::components::StructureData::set_abego(const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_alias(*args, **kwargs)

Overloaded function.

  1. set_alias(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, alias_name: str, segment_name: str, resi: int) -> None

sets an “alias” for a particular residue inside a segment which allows for it to be easily accessed

C++: protocols::denovo_design::components::StructureData::set_alias(const std::string &, const std::string &, const unsigned long) –> void

  1. set_alias(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, alias_name: str, resi: int) -> None

sets an “alias” for a particular residue which allows for it to be easily accessed

C++: protocols::denovo_design::components::StructureData::set_alias(const std::string &, const unsigned long) –> void

set_cutpoint(*args, **kwargs)

Overloaded function.

  1. set_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid: int) -> None

marks the ith residue as a cutpoint

C++: protocols::denovo_design::components::StructureData::set_cutpoint(const unsigned long) –> void

  1. set_cutpoint(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg: str, resi: int) -> None

marks the resi-th residue of segment as a cutpoint

C++: protocols::denovo_design::components::StructureData::set_cutpoint(const std::string &, const long) –> void

set_data_int(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str, val: int) None

sets real number data

C++: protocols::denovo_design::components::StructureData::set_data_int(const std::string &, const std::string &, const int) –> void

set_data_real(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str, val: float) None

sets real number data

C++: protocols::denovo_design::components::StructureData::set_data_real(const std::string &, const std::string &, const double) –> void

set_data_str(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment_id: str, data_name: str, val: str) None

sets real number data

C++: protocols::denovo_design::components::StructureData::set_data_str(const std::string &, const std::string &, const std::string &) –> void

set_id(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id_str: str) None

sets id name

C++: protocols::denovo_design::components::StructureData::set_id(const std::string &) –> void

set_movable_group(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id: str, mg: int) None

sets movable group of a segment

C++: protocols::denovo_design::components::StructureData::set_movable_group(const std::string &, const unsigned long) –> void

set_ss(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid: int, ss_type: str) None

sets secondary structure for residue resid

C++: protocols::denovo_design::components::StructureData::set_ss(const unsigned long, const char) –> void

set_template_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment: str, template_pose: pyrosetta.rosetta.core.pose.Pose, start_resid: int, stop_resid: int) None

attaches a template pose to the given segment

C++: protocols::denovo_design::components::StructureData::set_template_pose(const std::string &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

shared_from_this(self: pyrosetta.rosetta.basic.datacache.WriteableCacheableData) pyrosetta.rosetta.basic.datacache.WriteableCacheableData

C++: basic::datacache::WriteableCacheableData::shared_from_this() –> class std::shared_ptr<class basic::datacache::WriteableCacheableData>

slice(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segments: pyrosetta.rosetta.std.set_std_string_t, force_padding: bool) pyrosetta.rosetta.protocols.denovo_design.components.StructureData
Returns a StructureData containing only the given segments

The resulting StructureData will contain all data from the current

C++: protocols::denovo_design::components::StructureData::slice(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &, const bool) const –> class protocols::denovo_design::components::StructureData

ss(*args, **kwargs)

Overloaded function.

  1. ss(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) -> str

return secondary structure string

C++: protocols::denovo_design::components::StructureData::ss() const –> const std::string &

  1. ss(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid: int) -> str

abego of residue resid

C++: protocols::denovo_design::components::StructureData::ss(const unsigned long) const –> char

substitute_variables(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, input: pyrosetta.rosetta.std.istream) str

given an input stream, substitute all variables

variables are of the form: %%SEGMENTNAME#residue%% SEGMENTNAME = name of the segment residue = local residue number within the segment The substituted value will be an core::Size corresponding to the pose residue

C++: protocols::denovo_design::components::StructureData::substitute_variables(std::istream &) const –> std::string

termini(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, seg: str) Tuple[str, str]

returns n and c terminal segments of the chain which includes seg

C++: protocols::denovo_design::components::StructureData::termini(const std::string &) const –> struct std::pair<std::string, std::string >

update_numbering(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

updates numbering based on the saved order of Segment objects

C++: protocols::denovo_design::components::StructureData::update_numbering() –> void

upper_anchor(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, id_val: str) int

returns c-terminal residue of the chain represented by given string

C++: protocols::denovo_design::components::StructureData::upper_anchor(const std::string &) const –> unsigned long

write(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, os: pyrosetta.rosetta.std.ostream) None

C++: protocols::denovo_design::components::StructureData::write(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator

Bases: pyrosetta.rosetta.basic.datacache.WriteableCacheableDataCreator

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator, : pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator

C++: protocols::denovo_design::components::StructureDataCreator::operator=(const class protocols::denovo_design::components::StructureDataCreator &) –> class protocols::denovo_design::components::StructureDataCreator &

create_data(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator, in: pyrosetta.rosetta.std.istream) pyrosetta.rosetta.basic.datacache.WriteableCacheableData

C++: protocols::denovo_design::components::StructureDataCreator::create_data(std::istream &) const –> class std::shared_ptr<class basic::datacache::WriteableCacheableData>

keyname(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataCreator) str

C++: protocols::denovo_design::components::StructureDataCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_denovo_design_components_StructureDataFactory_t

Singleton for creating StructureData objects

attach_observer(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) None

attaches cacheable observer. Sets up cached SD if there isn’t one

C++: protocols::denovo_design::components::StructureDataFactory::attach_observer(class core::pose::Pose &) const –> void

clear_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) None
clears all structuredata information (including cached xml) from

this pose.

C++: protocols::denovo_design::components::StructureDataFactory::clear_from_pose(class core::pose::Pose &) const –> void

create_from_cacheable_data(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, raw_stream: pyrosetta.rosetta.std.istream) pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates from CacheableData stream

C++: protocols::denovo_design::components::StructureDataFactory::create_from_cacheable_data(std::istream &) const –> class protocols::denovo_design::components::StructureData

create_from_motifs(*args, **kwargs)

Overloaded function.

  1. create_from_motifs(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, motif_str: str) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates a StructureData from a motif string

String of secstruct/abego motifs (e.g. “1LX-5EB-2LG-5EB-1LA-1LB-1LG-10HA-1LX” )

StructureData containing one segment per motif with the specified

secondary structure and abego. Each motif is connected to the previous and next motifs. Segments are named by their secondary structure (e.g. L01, E01, L02, E02, L03, H01, L04 )

C++: protocols::denovo_design::components::StructureDataFactory::create_from_motifs(const std::string &) const –> class protocols::denovo_design::components::StructureData

  1. create_from_motifs(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, motif_str: str, prefix: str) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates a StructureData from a motif string, optionally prefixing a string to the

name of each segment

String of secstruct/abego motifs (e.g. “1LX-5EB-2LG-5EB-1LA-1LB-1LG-10HA-1LX” )

Name to be prepended before the segment names. If empty,

names will be as [ L01, E01, L02, … ]. If set to “myprefix”, names

will be as [ myprefix.L01, myprefix.E01, … ]

StructureData containing one segment per motif with the specified

secondary structure and abego. Each motif is connected to the previous and next motifs. Segments are named by their secondary structure (e.g. L01, E01, L02, E02, L03, H01, L04 )

C++: protocols::denovo_design::components::StructureDataFactory::create_from_motifs(const std::string &, const std::string &) const –> class protocols::denovo_design::components::StructureData

create_from_pose(*args, **kwargs)

Overloaded function.

  1. create_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

retrieves a StructureData object from the pose data cache

Creates a StructureData using the pose (but doesn’t store it) if the cached StructureData is not present

The input pose

C++: protocols::denovo_design::components::StructureDataFactory::create_from_pose(const class core::pose::Pose &) const –> class protocols::denovo_design::components::StructureData

  1. create_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> pyrosetta.rosetta.protocols.denovo_design.components.StructureData

retrieves a StructureData object from the pose data cache

Creates a StructureData using the pose (but doesn’t store it) if the cached StructureData is not present. Adds id_val as a prefix for all new segments

The input pose

A prefix to be added to the segments in the pose. For example, if

prefix is empty, the first helix would be named ‘H01’, but if prefix is set to ‘pose1’, the first helix will be named ‘pose.H01’

C++: protocols::denovo_design::components::StructureDataFactory::create_from_pose(const class core::pose::Pose &, const std::string &) const –> class protocols::denovo_design::components::StructureData

create_from_remarks(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, rem: pyrosetta.rosetta.core.io.Remarks) pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates SD from description stored in PDB remarks

C++: protocols::denovo_design::components::StructureDataFactory::create_from_remarks(const class core::io::Remarks &) const –> class protocols::denovo_design::components::StructureData

create_from_xml(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, xmltag: pyrosetta.rosetta.std.istream) pyrosetta.rosetta.protocols.denovo_design.components.StructureData

creates a StructureData from an xml stringstream

C++: protocols::denovo_design::components::StructureDataFactory::create_from_xml(std::istream &) const –> class protocols::denovo_design::components::StructureData

detach_observer(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) None

detaches cacheable observer and removes from observable cache

C++: protocols::denovo_design::components::StructureDataFactory::detach_observer(class core::pose::Pose &) const –> void

get_from_const_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from the pose observable cache

Creates a StructureData using the pose (but doesn’t attach it) if the cached StructureData could not be retrieved properly

C++: protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(const class core::pose::Pose &) const –> const class protocols::denovo_design::components::StructureData &

get_from_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.denovo_design.components.StructureData
retrieves a StructureData object from the pose observable cache

creates one if necessary

C++: protocols::denovo_design::components::StructureDataFactory::get_from_pose(class core::pose::Pose &) const –> const class protocols::denovo_design::components::StructureData &

static get_instance() protocols::denovo_design::components::StructureDataFactory

C++: utility::SingletonBase<protocols::denovo_design::components::StructureDataFactory>::get_instance() –> class protocols::denovo_design::components::StructureDataFactory *

has_cached_data(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) bool

checks whether StructureData is stored in the pose’s datacache

C++: protocols::denovo_design::components::StructureDataFactory::has_cached_data(const class core::pose::Pose &) const –> bool

observer_attached(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) bool
checks for a StructureData in the pose observer cache

Returns true if one is found, false otherwise

C++: protocols::denovo_design::components::StructureDataFactory::observer_attached(const class core::pose::Pose &) const –> bool

retrieve_observer(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose) protocols::denovo_design::components::StructureDataObserver
returns observer pointer if the pose has one cached

pointer returned can be null if no StructureData is present in the cache

C++: protocols::denovo_design::components::StructureDataFactory::retrieve_observer(const class core::pose::Pose &) const –> class std::shared_ptr<const class protocols::denovo_design::components::StructureDataObserver>

save_into_pose(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataFactory, pose: pyrosetta.rosetta.core.pose.Pose, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None
stores the data of this permutation into a pose for later retrieval

StructureData stored in a pose this way can be retrieved by calling get_from_pose(), or get_from_const_pose()

C++: protocols::denovo_design::components::StructureDataFactory::save_into_pose(class core::pose::Pose &, const class protocols::denovo_design::components::StructureData &) const –> void

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver

Bases: pyrosetta.rosetta.core.pose.datacache.CacheableObserver

a cacheable observer that keeps track of what length events occured

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver, : pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver

C++: protocols::denovo_design::components::StructureDataObserver::operator=(const class protocols::denovo_design::components::StructureDataObserver &) –> class protocols::denovo_design::components::StructureDataObserver &

attach_to(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver, pose: pyrosetta.rosetta.core.pose.Pose) None
attach to Pose/Conformation

Derived classes do not overload this method – see attach_impl() instead.

C++: core::pose::datacache::CacheableObserver::attach_to(class core::pose::Pose &) –> void

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) pyrosetta.rosetta.core.pose.datacache.CacheableObserver

clone this object

C++: protocols::denovo_design::components::StructureDataObserver::clone() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

create(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) pyrosetta.rosetta.core.pose.datacache.CacheableObserver

create a new instance of this object

C++: protocols::denovo_design::components::StructureDataObserver::create() –> class std::shared_ptr<class core::pose::datacache::CacheableObserver>

detach_from(self: pyrosetta.rosetta.core.pose.datacache.CacheableObserver) None

detach from Pose/Conformation

Derived classes do not overload this method – see

detach_impl() instead.

C++: core::pose::datacache::CacheableObserver::detach_from() –> void

is_attached(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataObserver) bool

is this observer attached to a Pose/Conformation?

C++: protocols::denovo_design::components::StructureDataObserver::is_attached() const –> bool

C++: protocols::denovo_design::components::StructureDataObserver::set_length_event_link(const class utility::signals::Link &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

Bases: pybind11_builtins.pybind11_object

Classes for altering StructureData objects on the fly

apply(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None

C++: protocols::denovo_design::components::StructureDataPerturber::apply(class protocols::denovo_design::components::StructureData &) –> void

assign(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, : pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::operator=(const class protocols::denovo_design::components::StructureDataPerturber &) –> class protocols::denovo_design::components::StructureDataPerturber &

clone(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::clone() const –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

static create(tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber

C++: protocols::denovo_design::components::StructureDataPerturber::create(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> class std::shared_ptr<class protocols::denovo_design::components::StructureDataPerturber>

enumerate(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) pyrosetta.rosetta.utility.vector1_utility_vector1_std_shared_ptr_const_protocols_denovo_design_components_Segment_std_allocator_std_shared_ptr_const_protocols_denovo_design_components_Segment_t

C++: protocols::denovo_design::components::StructureDataPerturber::enumerate(const class protocols::denovo_design::components::StructureData &) const –> class utility::vector1<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > >, class std::allocator<class utility::vector1<class std::shared_ptr<const class protocols::denovo_design::components::Segment>, class std::allocator<class std::shared_ptr<const class protocols::denovo_design::components::Segment> > > > >

ignored(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, segment_name: str) bool

C++: protocols::denovo_design::components::StructureDataPerturber::ignored(const std::string &) const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::denovo_design::components::StructureDataPerturber::parse_my_tag(const class utility::tag::Tag &, class basic::datacache::DataMap &) –> void

set_ignore_segments(self: pyrosetta.rosetta.protocols.denovo_design.components.StructureDataPerturber, ignore_set: pyrosetta.rosetta.std.set_std_string_t) None

C++: protocols::denovo_design::components::StructureDataPerturber::set_ignore_segments(const class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

class pyrosetta.rosetta.protocols.denovo_design.components.StructureSlice

Bases: pybind11_builtins.pybind11_object

class pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected

Bases: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild

add_rcg(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, rcg: protocols::forge::remodel::RemodelConstraintGenerator) None

C++: protocols::forge::components::VarLengthBuild::add_rcg(class std::shared_ptr<class protocols::forge::remodel::RemodelConstraintGenerator>) –> void

add_setup_mover(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, mover_in: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::forge::components::VarLengthBuild::add_setup_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

add_user_provided_mover(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, mover_in: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::forge::components::VarLengthBuild::add_user_provided_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

apply(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, pose: pyrosetta.rosetta.core.pose.Pose) None

run protocol on given Pose

if procedure successful, return Pose with modifications and a

sealed fold tree, otherwise return Pose with modifications and the in-progress cut fold tree

Before invoking this function it’s best to make sure

the secondary structure in the Pose is marked via the method that you would prefer, e.g. by Dssp (protocols::jumping::Dssp), by the old Rosetta++ binning method (core::pose::set_ss_from_phipsi) or by external method such as reading in a file.

C++: protocols::forge::components::VarLengthBuild::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

cache_fragments(*args, **kwargs)

Overloaded function.

  1. cache_fragments(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

cache fragments after picking? (default true)

If true, will cache fragments and reuse them upon each

apply() call instead of repicking every time.

C++: protocols::forge::components::VarLengthBuild::cache_fragments() const –> bool

  1. cache_fragments(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

cache fragments after picking?

If true, will cache fragments and reuse them upon each

apply() call instead of repicking every time.

C++: protocols::forge::components::VarLengthBuild::cache_fragments(const bool) –> void

clear_fragments(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

clear any currently cached fragments

C++: protocols::forge::components::VarLengthBuild::clear_fragments() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clear_rcgs(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

C++: protocols::forge::components::VarLengthBuild::clear_rcgs() –> void

clear_setup_movers(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

C++: protocols::forge::components::VarLengthBuild::clear_setup_movers() –> void

clear_user_provided_movers(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

C++: protocols::forge::components::VarLengthBuild::clear_user_provided_movers() –> void

clone(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::forge::components::VarLengthBuild::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) pyrosetta.rosetta.protocols.moves.Mover

create a new instance of this type of object

C++: protocols::forge::components::VarLengthBuild::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) str

C++: protocols::forge::components::VarLengthBuild::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

ignore_cmdline_enzdes_cstfile(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) None

C++: protocols::forge::components::VarLengthBuild::ignore_cmdline_enzdes_cstfile(const bool) –> void

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

loop_mover_fold_tree_constant(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) None

C++: protocols::forge::components::VarLengthBuild::loop_mover_fold_tree_constant(const bool) –> void

loop_mover_str(*args, **kwargs)

Overloaded function.

  1. loop_mover_str(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

the string id of the loop mover to use

(default “RemodelLoopMover”)

“RemodelLoopMover” for the forge RemodelLoopMover, otherwise a

string recognized by create_loop_mover() in the “LoopMoverFactory”.

C++: protocols::forge::components::VarLengthBuild::loop_mover_str() const –> const std::string &

  1. loop_mover_str(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, str: str) -> None

set the loop mover to use via string

use “RemodelLoopMover” for the forge RemodelLoopMover,

otherwise set it to a string recognized by create_loop_mover() in the “LoopMoverFactory”.

C++: protocols::forge::components::VarLengthBuild::loop_mover_str(const std::string &) –> void

manager(*args, **kwargs)

Overloaded function.

  1. manager(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> pyrosetta.rosetta.protocols.forge.build.BuildManager

build manager

C++: protocols::forge::components::VarLengthBuild::manager() const –> const class protocols::forge::build::BuildManager &

  1. manager(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, manager: pyrosetta.rosetta.protocols.forge.build.BuildManager) -> None

set build manager; also clears any cached fragments

C++: protocols::forge::components::VarLengthBuild::manager(const class protocols::forge::build::BuildManager &) –> void

max_linear_chainbreak(*args, **kwargs)

Overloaded function.

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> float

return the highest linear chainbreak score a chainbreak can have

and still be considered closed

default 0.07

C++: protocols::forge::components::VarLengthBuild::max_linear_chainbreak() const –> double

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, tol: float) -> None

set the highest linear chainbreak score a chainbreak can have

and still be considered closed

C++: protocols::forge::components::VarLengthBuild::max_linear_chainbreak(const double) –> void

static name() str

C++: protocols::moves::Mover::name() –> std::string

new_secondary_structure_override(*args, **kwargs)

Overloaded function.

  1. new_secondary_structure_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

full sequence string with length corresponding to the new

modified pose used to pick secondary structure biased fragments.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_secondary_structure_override() const –> const std::string &

  1. new_secondary_structure_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, str: str) -> None

full sequence string with length corresponding to the new

modified pose used to pick secondary structure biased fragments.

String with length equals to the new modified pose.

See remarks for help on how to determine this. String is allowed to be empty, in which case it will clear the setting.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_secondary_structure_override(const std::string &) –> void

new_sequence_override(*args, **kwargs)

Overloaded function.

  1. new_sequence_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

full amino acid string with length corresponding to the new

modified pose used to pick sequence biased fragments.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_sequence_override() const –> const std::string &

  1. new_sequence_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, str: str) -> None

full amino acid string with length corresponding to the new

modified pose used to pick sequence biased fragments.

String with length equals to the new modified pose.

See remarks for help on how to determine this. String is allowed to be empty, in which case it will clear the setting.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_sequence_override(const std::string &) –> void

num_fragpick(*args, **kwargs)

Overloaded function.

  1. num_fragpick(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> int

the number of fragments to pick at each position

(default 200)

C++: protocols::forge::components::VarLengthBuild::num_fragpick() const –> unsigned long

  1. num_fragpick(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, num: int) -> None

the number of fragments to pick at each position (default 200)

C++: protocols::forge::components::VarLengthBuild::num_fragpick(const unsigned long) –> void

original_sequence(*args, **kwargs)

Overloaded function.

  1. original_sequence(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

full sequence string corresponding to original input pose

used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

C++: protocols::forge::components::VarLengthBuild::original_sequence() –> const std::string &

  1. original_sequence(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, seq: str) -> None

full sequence string corresponding to original input pose

used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

C++: protocols::forge::components::VarLengthBuild::original_sequence(const std::string &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pick_fragments_public(self: pyrosetta.rosetta.protocols.denovo_design.components.VLBProtected, complete_ss: str, complete_aa: str, complete_abego: pyrosetta.rosetta.utility.vector1_std_string, interval: protocols::forge::build::Interval, frag_length: int, n_frags: int) pyrosetta.rosetta.core.fragment.FrameList

pick fragments of a given length, padding when necessary

The complete secondary structure string, typically from a Pose.

The complete amino acid string, typically from a Pose;

can be empty. If empty, sequence bias is not used to pick fragments.

The complete abego string, typically from a setter, set_abego

The interval [left, right] to pick fragments from; Pose

numbering (i.e. 1-based indexing).

The desired length of the fragments

The number of fragments to pick per position.

C++: protocols::denovo_design::components::VLBProtected::pick_fragments_public(const std::string &, const std::string &, const class utility::vector1<std::string, class std::allocator<std::string > > &, const struct protocols::forge::build::Interval &, const unsigned long, const unsigned long) –> class core::fragment::FrameList

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

recover_original_on_failure(*args, **kwargs)

Overloaded function.

  1. recover_original_on_failure(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

at the end of apply(), reset the Pose to the original Pose if

mover was not successful? (default true)

C++: protocols::forge::components::VarLengthBuild::recover_original_on_failure() const –> bool

  1. recover_original_on_failure(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

at the end of apply(), reset the Pose to the original Pose if

mover was not successful?

C++: protocols::forge::components::VarLengthBuild::recover_original_on_failure(const bool) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

restart_mode(*args, **kwargs)

Overloaded function.

  1. restart_mode(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

Flag to turn on restart mode, in which VLB assumes that the Pose

fed to it during apply() has already been modified by the manager. (default False)

In restart mode, VLB only runs the manager’s dummy modify

capability during apply() to get the mapping info.

C++: protocols::forge::components::VarLengthBuild::restart_mode() const –> bool

  1. restart_mode(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

Flag to turn on restart mode, in which VLB assumes that the Pose

fed to it during apply() has already been modified by the manager. (default False)

In restart mode, VLB only runs the manager’s dummy modify

capability during apply() to get the mapping info.

C++: protocols::forge::components::VarLengthBuild::restart_mode(const bool) –> void

scorefunction(*args, **kwargs)

Overloaded function.

  1. scorefunction(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set ScoreFunction used during build

C++: protocols::forge::components::VarLengthBuild::scorefunction(const class core::scoring::ScoreFunction &) –> void

  1. scorefunction(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set ScoreFunction used during build

C++: protocols::forge::components::VarLengthBuild::scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_abego(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, abego: pyrosetta.rosetta.utility.vector1_std_string) None

set abego definition for fragments

C++: protocols::forge::components::VarLengthBuild::set_abego(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

use_fullmer(*args, **kwargs)

Overloaded function.

  1. use_fullmer(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

also use fragments spanning the entire length of a loop?

(default false)

C++: protocols::forge::components::VarLengthBuild::use_fullmer() const –> bool

  1. use_fullmer(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

also use fragments spanning the entire length of a loop?

C++: protocols::forge::components::VarLengthBuild::use_fullmer(const bool) –> void

vall_memory_usage(*args, **kwargs)

Overloaded function.

  1. vall_memory_usage(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum

option dictating whether to keep VallLibrary in memory or clear

it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY)

C++: protocols::forge::components::VarLengthBuild::vall_memory_usage() const –> enum protocols::forge::components::VLB_VallMemoryUsage::Enum

  1. vall_memory_usage(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, level: pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum) -> None

option dictating whether to keep VallLibrary in memory or clear

it under certain circumstances after picking fragments.

C++: protocols::forge::components::VarLengthBuild::vall_memory_usage(const enum protocols::forge::components::VLB_VallMemoryUsage::Enum) –> void

pyrosetta.rosetta.protocols.denovo_design.components.add_segments_for_chain(id_val: str, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, chain_ss: str, chain_abego: str, counts: pyrosetta.rosetta.protocols.denovo_design.components.SegmentCounts) None

Adds segments to the given SD

Parent ID of the segments. Can be empty

StructureData to be modified

Secondary structure of the full chain

Abego for the full chain

Secondary structure element counters for naming segments

C++: protocols::denovo_design::components::add_segments_for_chain(const std::string &, class protocols::denovo_design::components::StructureData &, const std::string &, const std::string &, class protocols::denovo_design::components::SegmentCounts &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.add_to_pose(newpose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose, s_start: int, s_stop: int) int

C++: protocols::denovo_design::components::add_to_pose(class std::shared_ptr<class core::pose::Pose>, const class core::pose::Pose &, unsigned long, unsigned long) –> int

pyrosetta.rosetta.protocols.denovo_design.components.append_new_chain_from_template_segment(pose: pyrosetta.rosetta.core.pose.Pose, segment: protocols::denovo_design::components::Segment) None

C++: protocols::denovo_design::components::append_new_chain_from_template_segment(class core::pose::Pose &, const class protocols::denovo_design::components::Segment &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.append_new_residues(pose: pyrosetta.rosetta.core.pose.Pose, num_residues: int, insert_pos: int, anchor: int, type: str, upper_dihedrals: protocols::denovo_design::components::ResidueDihedrals) None

C++: protocols::denovo_design::components::append_new_residues(class core::pose::Pose &, const unsigned long, unsigned long, const unsigned long, const std::string &, const class protocols::denovo_design::components::ResidueDihedrals &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.append_residues_from_template_segment(pose: pyrosetta.rosetta.core.pose.Pose, prev_segment: protocols::denovo_design::components::Segment, segment: protocols::denovo_design::components::Segment) None

C++: protocols::denovo_design::components::append_residues_from_template_segment(class core::pose::Pose &, const class protocols::denovo_design::components::Segment &, const class protocols::denovo_design::components::Segment &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.canonicalize(orientations: str, lengths: str) Tuple[str, str]

C++: protocols::denovo_design::components::canonicalize(const std::string &, const std::string &) –> struct std::pair<std::string, std::string >

pyrosetta.rosetta.protocols.denovo_design.components.choose_canonical(l1: str, l2: str) str

C++: protocols::denovo_design::components::choose_canonical(const std::string &, const std::string &) –> const std::string &

pyrosetta.rosetta.protocols.denovo_design.components.clean_for_storage(ss: str) None

prepare a string to be stored in the string datacache

C++: protocols::denovo_design::components::clean_for_storage(std::string &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.clean_from_storage(st: str) None

prepare a string that was stored in string datacache

C++: protocols::denovo_design::components::clean_from_storage(std::string &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.extract_sheets_from_pose(pose: pyrosetta.rosetta.core.pose.Pose, spairs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_fldsgn_topology_StrandPairing_t, ss_info: protocols::fldsgn::topology::SS_Info2, idealize: bool) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::denovo_design::components::extract_sheets_from_pose(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing>, class std::allocator<class std::shared_ptr<class protocols::fldsgn::topology::StrandPairing> > > &, const class protocols::fldsgn::topology::SS_Info2 &, const bool) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

pyrosetta.rosetta.protocols.denovo_design.components.extract_sheets_from_strandlist(strands: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, nstrands: int) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::denovo_design::components::extract_sheets_from_strandlist(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, const unsigned long) –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

pyrosetta.rosetta.protocols.denovo_design.components.find_orientations_and_lengths(pose: pyrosetta.rosetta.core.pose.Pose) Tuple[str, str]

gets a pair of strings, which refer to orientations, and lengths/shifts. Pose secstruct MUST be set

C++: protocols::denovo_design::components::find_orientations_and_lengths(const class core::pose::Pose &) –> struct std::pair<std::string, std::string >

pyrosetta.rosetta.protocols.denovo_design.components.get_closest_chain_ending(chain_endings: pyrosetta.rosetta.utility.vector1_unsigned_long, total_residue: int, end_res: int) int

C++: protocols::denovo_design::components::get_closest_chain_ending(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.components.make_strand_info_str(lengths: pyrosetta.rosetta.utility.vector1_unsigned_long, shifts: pyrosetta.rosetta.utility.vector1_long) str

creates a string key for lengths/shifts based on the given vectors for strand lengths and register shifts

C++: protocols::denovo_design::components::make_strand_info_str(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<long, class std::allocator<long> > &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.components.modify_ft_for_residue_insertion(pose: pyrosetta.rosetta.core.pose.Pose, safe_res: int) pyrosetta.rosetta.core.kinematics.FoldTree

modifies teh ft in the pose, returns the original

C++: protocols::denovo_design::components::modify_ft_for_residue_insertion(class core::pose::Pose &, const unsigned long) –> class core::kinematics::FoldTree

pyrosetta.rosetta.protocols.denovo_design.components.num_strands(pose: pyrosetta.rosetta.core.pose.Pose) int

counts number of strands based on number of jumps. Pose must be a disconnected sheet

C++: protocols::denovo_design::components::num_strands(const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.denovo_design.components.parse_lengths(lengths: str) Tuple[pyrosetta.rosetta.utility.vector1_unsigned_long, pyrosetta.rosetta.utility.vector1_int]

C++: protocols::denovo_design::components::parse_lengths(const std::string &) –> struct std::pair<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<int, class std::allocator<int> > >

pyrosetta.rosetta.protocols.denovo_design.components.parse_orientations(orientations: str) pyrosetta.rosetta.utility.vector1_bool

C++: protocols::denovo_design::components::parse_orientations(const std::string &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.protocols.denovo_design.components.prepend_new_residues(pose: pyrosetta.rosetta.core.pose.Pose, num_residues: int, insert_pos: int, anchor: int, type: str, lower_dihedrals: protocols::denovo_design::components::ResidueDihedrals) None

C++: protocols::denovo_design::components::prepend_new_residues(class core::pose::Pose &, const unsigned long, unsigned long, const unsigned long, const std::string &, const class protocols::denovo_design::components::ResidueDihedrals &) –> void

pyrosetta.rosetta.protocols.denovo_design.components.reverse_chains(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pose.Pose

C++: protocols::denovo_design::components::reverse_chains(const class core::pose::Pose &) –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.denovo_design.components.reverse_lengths(orientations: str, lengths: str) str

C++: protocols::denovo_design::components::reverse_lengths(const std::string &, const std::string &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.components.reverse_orientations(orient: str) str

C++: protocols::denovo_design::components::reverse_orientations(const std::string &) –> std::string

pyrosetta.rosetta.protocols.denovo_design.components.truncate_abego(complete_abego: pyrosetta.rosetta.utility.vector1_std_string, closest_chain_ending: int) pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::denovo_design::components::truncate_abego(const class utility::vector1<std::string, class std::allocator<std::string > > &, const unsigned long) –> class utility::vector1<std::string, class std::allocator<std::string > >